ArticleNucleic acids research2014
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
102 citing papers in PubMed, 213 citations in OpenAlex.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.Molecular cell · 2026Article
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.Nucleic acids research · 2025Article
- Building a better bridge between models and experimental data for DNA.Biophysical journal · 2025Article
- Navigating the complexity of p53-DNA binding: implications for cancer therapy.Biophysical reviews · 2024Review
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- DNA simulation benchmarks revealed with the accumulation of high-resolution structures.Biophysical reviews · 2024Review
- MD-DATA: the legacy of the ABC Consortium.Biophysical reviews · 2024Article
- Multiscale simulations of DNA from electrons to nucleosomes: 22 years of the Ascona B-DNA Consortium.Biophysical reviews · 2024Review
- Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications.NAR genomics and bioinformatics · 2024Article
- A commentary on the ABC consortium and its impact on the development of mesoscopic models of DNA.Biophysical reviews · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Mechanical codes of chemical-scale specificity in DNA motifs.Chemical science · 2023Article
- Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism.Nucleic acids research · 2023Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 14 institutions in 7 countries.
Funding
Abstract
We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.